Hi, I am a fifth-year Ph.D. student in Biomedical Informatics Division under the supervision of Dr. Bruce Aronow at Cincinnati Children’s Hospital. I am currently visiting Shu lab at Massachusetts General Hospital, where I am learning spatial transcriptomics technologies.
As an enthusiastic researcher, I am passionate about harnessing advanced computational techniques to unveil the biological mechanisms hidden within high-throughput sequencing and high-content imaging data, with a specific focus on image-based spatial profiling. My present work primarily centers around the development of cutting-edge deep learning models tailored to image-based spatial omics data (Jin*, Zhang* et al., bioRxiv, 2023) and the analysis of temporal perturbation patterns in single-cell experiments (Jin et al., Briefings in Bioinformatics, 2022). My commitment extends to active involvement in the experimental design of spatial multi-omics experiments, and I possess a wealth of experience in exploring single cell data across various biological systems and diseases, including HLHS (Xu, Jin et al., Cell Stem Cell, 2022), schizophrenia (Sebastian*, Jin* et al. Nat Communications, 2023), among others.
I am particularly interested in cutting-edge bioengineering innovations, such as image-based spatial transcriptomics and optical molecular recording. Collaborating with Dr. Jian Shu, we are devotedly developing innovative methods for in-situ molecular recording through microscopy.
With expertise in computational biology and a strong interest in bioengineering, my ultimate goal is to advance our understanding of neuroscience and cancer biology by implementing cutting-edge computational methods with emerging new molecular recording technologies.
2022 - Present, Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School,
2018 - Present, Department of Biomedical Informatics, Cincinnati Children's Hospital, University of Cincinnati,
2014 - 2018, Department of Life Sciences, Zhejiang University,
Bachelor of Biological Science
Bering: joint cell segmentation and annotation for spatial transcriptomics with transferred graph embeddings
Kang Jin*, Zuobai Zhang*, Ke Zhang, Francesca Viggiani, Claire Callahan, Jian Tang, Bruce J. Aronow, Jian Shu
CellDrift: Inferring Perturbation Responses in Temporally-Sampled Single Cell Data
Kang Jin, Dan Schnell, Guangyuan Li, Nathan Salomonis, Surya Prasath, Rhonda Szczesniak, Bruce J Aronow
Briefings in Bioinformatics (2022).
Single cell transcriptomic profiling of human brain organoids reveals developmental timing- and cell-type-specific vulnerabilities induced by NRXN1 CNVs in schizophrenia
Rebecca Sebastian*, Kang Jin*, Narciso Pavon, Ruby Bansal, Andrew Potter, Yoonjae Song, Juliana Babu, Rafael Gabriel, Yubing Sun, Bruce Aronow, ChangHui Pak
Nature Communications (2023).
An interactive single cell web portal identifies gene and cell networks in COVID-19 host responses
Kang Jin, Eric E. Bardes, Alexis Mitelpunkt, Jake Y. Wang, Surbhi Bhatnagar, Soma Sengupta, Daniel Pomeranz Krummel, Marc E. Rothenberg, Bruce J. Aronow
Uncompensated mitochondrial oxidative stress underlies heart failure in an iPSC-derived model of congenital heart disease
Xinxiu Xu, Kang Jin, Abha S Bais, Wenjuan Zhu, Hisato Yagi, Timothy N Feinstein, Phong K Nguyen, Joseph D Criscione, Xiaoqin Liu, Gisela Beutner, Kalyani B Karunakaran, Krithika S Rao, Haoting He, Phillip Adams, Catherine K Kuo, Dennis Kostka, Gloria S Pryhuber, Sruti Shiva, Madhavi K Ganapathiraju, George A Porter Jr, Jiuann-Huey Ivy Lin, Bruce Aronow, Cecilia W Lo
Cell Stem Cell (2022).
Identification of distinct tumor cell populations and key genetic mechanisms through single cell sequencing in hepatoblastoma
Alexander Bondoc*, Kathryn Glaser*, Kang Jin*, Charissa Lake, Stefano Cairo, James Geller, Gregory Tiao, Bruce Aronow
Communications Biology (2021).
Guided construction of single cell reference for human and mouse lung
Minzhe Guo, Michael P Morley, Yixin Wu, Yina Du, Shuyang Zhao, Andrew Wagner, Michal Kouril, Kang Jin, ..., Yan Xu
Nature Communications (2023).
KAT5 activity regulates G0-like states in human gliomas
Anca B. Mihalas, Sonali Arora, Samantha A. O’Connor, Heather M. Feldman, John Bassett, Kelly Mitchell, Kang Jin, ..., Patrick J. Paddisons
LungMAP Portal Ecosystem: Systems-Level Exploration of the Lung
Nathan Gaddis, Joshua Fortriede, Minzhe Guo, ..., Kang Jin, ..., Nathan Salomonis, NHLBI LungMAP Consortium
American Journal of Respiratory Cell and Molecular Biology (2022).
Loss of Neurodevelopmental Gene CASK Disrupts Neural Connectivity in Human Cortical Excitatory Neurons
Danny McSweeney, Rafael Gabriel, Kang Jin, Zhiping P Pang, Bruce J Aronow, ChangHui Pak
A census of the lung: CellCards from LungMAP
Xin Sun, Anne-Karina Perl, Rongbo Li, ..., Kang Jin, ..., Edward E Morrisey, NHLBI LungMAP Consortium
Developmental Cell (2022).
Cross-platform validation of neurotransmitter release impairments in schizophrenia patient-derived NRXN1-mutant neurons
ChangHui Pak, Tamas Danko, Vincent R. Mirabella, Jinzhao Wang, Yingfei Liu, Madhuri Vangipuram, Sarah Grieder, Xianglong Zhang, Thomas Ward, Yu-Wen Alvin Huang, Kang Jin, ..., Thomas C. Südhof
Functional immune deficiency syndrome via intestinal infection in COVID-19
Erica T. Prates, Michael R. Garvin, Mirko Pavicic, Piet Jones, Manesh Shah, Christiane Alvarez, David Kainer, Omar Demerdash, B Kirtley Amos, Armin Geiger, John Pestian, Kang Jin, Alexis Mitelpunkt, Eric Bardes, Bruce Aronow, Daniel Jacobson
Predicted Arabidopsis interactome resource and gene set linkage analysis: a transcriptomic analysis resource
Heng Yao, Xiaoxuan Wang, Pengcheng Chen, Ling Hai, Kang Jin, Lixia Yao, Chuanzao Mao, Xin Chen
Plant Physiology (2018).
Bering: Cell segmentation and annotation in high-resolution spatial transcriptomics data
ToppCell: Single-cell gene module exploratory platform
CellDrift: Inferring Perturbation Responses in Temporally-Sampled Single Cell Data.
Bering: Gene colocalization-aware segmentation of image-based spatial transcriptomics using deep learning models (Wrapping up)
Digestion of BICCN Nature Paper Collections
A brift digestion of 16 BICCN papers published on Nature on Oct 2021, which introduced comprensive brain atlases and resources covering transcriptomic, epigenomic, morphogenic, eletrophysiological, spatial and other data.
Journal Club: The specious Art of Single Cell Genomics
Slide for a journal club, which covered an overview of current neighbor embedding methods and discussion about Dr. Lior Pachter's recent preprint on UMAP.